He is surrounded by controversy related to his radical calls for reforms and though he has been demoted from being a religious authority and considered to no longer be qualified for emulation as a Grand Ayatollah by The Qom Theological Lecturers Association (Jame-e-Modarressin). However, many influential Maraji such as Grand Ayatollah Ali al-Sistani, Naser Makarem Shirazi, Abdul-Karim Mousavi Ardebili and Hossein Noori Hamedani have mentioned that Ayatollah Sanei's followers can continue to regard him as their Marja'.[1] Despite the controversy, he has still many followers who continue to consider him as their Marja.[2]

"There is complete consensus on this issue. It is self-evident in Islam that it is prohibited to have nuclear bombs. It is eternal law, because the basic function of these weapons is to kill innocent people. This cannot be reversed.".[6]

Ayatollah Yousef Sanei said clerical authorities have quietly expressed opposition to the development of weapons of mass destruction for many years, and he described it as the reason that Iran never retaliated with chemical weapons when Saddam Hussein used them to kill Iranian troops and Iran-backed Kurds during the 1980- 88 Iran-Iraq war. "You cannot deliberately kill innocent people," he said.

He has declared that women have equal status in Islam. Like Zohreh Sefati, he believes that women can even become a marja' in Islam, i.e. that men and women can follow a female Islamic jurists' ijtihad.

During the 2009 Iranian election protests, rumours arose that he had issued a religious edict proclaiming that Mr. Ahmedinejad was "not the president and that it is forbidden to cooperate with his government." These rumours were reported as such by several internet news agencies.[8][9][10]

He is reported to have said during an August 12 speech at Gorgan that “Confession in prison and detention has not been and is not valid ... all persons who have somehow been involved in issuing these confessions are sharing same sin ... they will receive the retribution of their perfidious acts in this world and in a fair, righteous court.”[11]

According to one report, Saanei was likely to replace Hosein-Ali Montazeri as the leading clerical opponent of the regime and to be even more aggressive. Saanei declared the government illegitimate and warned that it "cannot reverse the situation in the country with terror, killing, torture and imprisonment."[12]

A day after the funeral procession of Montazeri, around 1,000 members of Iran's Basij militia and "plainclothes men" attacked offices of Saanei in the central shrine city of Qom, a reformist website reported on 22 December 2009. The plainclothes militiamen broke the windows of Sanei's office and insulted him and his staff and also beat up his staff. They also put up posters of Iran's supreme leader Ali Khamenei, who has been a staunch defender of hardline President Mahmoud Ahmadinejad's controversial June re-election and who ordered a post-election crackdown on opposition protests. Police sided with the militia and prevented Sanei’s supporters from defending his office, the website said. There was no immediate official comment. However, earlier on Tuesday, the semi-official Fars News Agency said pro-government theology students had staged a rally in Qom to protest "the insult against sanctities" during Montazeri's funeral procession. The demonstration ended outside Saanei's home, Fars said, but it was not clear whether it was linked to the attack on Sanei's house reported by the aforementioned reformist website. The demonstrators chanted "The city of Qom is no city for hypocrites," and signed a statement calling for Sanei to be defrocked, Fars reported. One of the signatories, cleric Ahmad Panahian, said: "The trenches of the hypocrites in Qom must be destroyed."[13][14]

On 3 October 2010, news sites linked with Iran’s political opposition movement reported that Saanei's website was blocked. According to The New York Times, "Internet users who attempted to access them ... were automatically redirected to a standard Iranian government filtering page which offers links to government-authorized web sites ... and the official web site of Iran’s Supreme Leader, Ayatollah Ali Khamenei."[15]

On 2 January 2010, a top clerical body in Qom, (The Qom Theological Lecturers Association, Jame-e-Modarressin), declared that Saanei no longer qualifies to be a marja al-taqlid, or a source of emulation — the highest clerical rank in Shia Islam. The body said that it had launched a yearlong investigation into the qualifications of Sanei in response to repetitive inquiries on the issue. In a statement bearing the signature of Ayatollah Mohammad Yazdi, the former head of Iran's judiciary, the body announced that the result of the investigation indicate that Sanei is not eligible to be a marja.[2]

Conservatives and traditionalist condemned this move by Ayatollah Mohammad Yazdi of Hoze Modaresin to disqualify Ayatollah Saanei as a Marja, questioned the authority of the government sanctioned and subsidized association, and pointed out that even a renowned Marja such as Ayatollah Sistani is not even listed by them as such.[16][17]